京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第18332号 / 農博第2057号 / 新制||農||1023(附属図書館) / 学位論文||H26||N4839(農学部図書室) / 31190 / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 植田 充美, 教授 渡邊 隆司, 教授 梅澤 俊明 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

CO2 fixation is a thermodynamically and kinetically challenging process, but nature has its own way of transforming CO2 into diverse organic molecules. Of our particular interest is 2-oxoacid:ferredoxin oxidoreductase (OFOR) that catalyzes the anaerobic, reversible inter-conversion of 2-oxoacids and CO2, making use of a small electron-transfer protein, ferredoxin (Fd), as the redox partner. This dissertation characterizes OFORs and Fds from organisms that exhibit different metabolic patterns and investigates how the interplay of OFOR and Fd could impact the fate of CO2 metabolism, asking the question What controls the catalytic bias of OFOR for CO2 evolution versus fixation? The study of OFORs and Fds from Desulfovibrio africanus and Hydrogenobacter thermophilus through an electrocatalytic assay reveals that the reduction potential of Fd is possibly associated with the biological function of OFOR and that CO2 fixation requires a low-potential electron donor. The Fd from H. thermophilus (HtFd1) is used as a model to probe the factors that govern iron-sulfur cluster potential. The dependence of OFOR activity on Fd potential is systematically studied with HtFd1 and its molecular variants through the electrocatalytic assay and a coupled enzyme assay. The results suggest there is a Fd “potential optimum” for OFOR-catalyzed CO2 fixation. The study of a 2-oxoglutarate:ferredoxin oxidoreductase (OGOR) and three Fds from Magnetococcus marinus MC-1 further highlights other factors such as the intramolecular electron-transfer within Fd and the electrostatic and hydrophobic interactions at the protein-protein interface in determining OFOR-Fd interaction. The characterization of an OGOR from M. marinus MC-1 (MmOGOR) also provides kinetic, structural and spectroscopic details for a CO2-fixing OFOR that contains only one iron-sulfur cluster. Overall, this work furthers the scientific understanding of how nature achieves CO2 fixation through supplying reducing equivalents and with enzymes as efficient catalysts, and how intermolecular electron-transfer mediated by protein-protein interaction could regulate enzyme catalysis. / 2019-10-08T00:00:00Z

Oceans are powered by active, metabolically diverse microorganisms, which are important in regulating biogeochemical cycles on Earth. Most of the ocean surface is often limited by nutrients, influencing bacterial growth and activities. Bacterial adaptation to fluctuating environmental conditions involves extensive reprogramming, and redirection of bacterial metabolism and physiology. In this thesis, I investigated the molecular mechanisms of bacterial adaptation strategies to sustain their growth and survival, focusing on the regulation of gene and protein expression in heterotrophic marine bacteria. Comparative proteomics analyses of the growth and non-growth conditions, uncovered central adaptations that marine bacteria employ to allow them to change their metabolism to support exponential growth in response to nutrients and to readjust to stationary phase under nutrient limitation. Our results highlight that during nutrient rich conditions three distinct bacteria lineages have great similarities in their proteome. On the other hand, we observed pronounced differences in behavior between taxa during stationary phase. Analyses of the proteorhodopsin containing bacterium Vibrio sp. AND4 during starvation showed that significantly improved survival in the light compared to darkness. Notably, proteins involved in promoting cell vitality and survival had higher relative abundance under light. In contrast, cells in the dark need to degrade their endogenous resources to support their basic cellular demands under starvation. Thus, light strongly influences how PR-containing bacteria organize their molecular composition in response to starvation. Study of alternative energy generation metabolisms in the Alphaproteobacteria Phaeobacter sp. MED193 showed that the addition of thiosulfate enhanced the bacterial growth yields. Concomitantly, inorganic sulfur oxidation gene expression increased with thiosulfate compared to controls. Moreover, thiosulfate stimulated protein synthesis and anaplerotic CO2 fixation. These findings imply that this bacterium could use their lithotrophic potential to gain additional energy from sulfur oxidation for both improving their growth and survival. This thesis concludes that analyses in model organisms under defined growth conditions gives invaluable knowledge about the regulatory networks and physiological strategies that ensure the growth and survival of heterotrophic bacteria. This is critically important for interpreting bacterial responses to dynamic environmental changes. Moreover, these analyses are crucial for understanding genetic and proteomic responses in microbial communities or uncultivated organisms in terms of defining ecological niches of planktonic bacteria

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第19781号 / 農博第2177号 / 新制||農||1041(附属図書館) / 学位論文||H28||N4997(農学部図書室) / 32817 / 京都大学大学院農学研究科農学専攻 / (主査)教授 白岩 立彦, 教授 奥本 裕, 教授 稲村 達也 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

El CO2 es una variable clave que afecta tanto al desarrollo como a la fisiología de las plantas, por lo que los incrementos derivados del cambio climático afectarán al crecimiento de los cultivos. Muchas de las respuestas fisiológicas observadas frente al aumento del CO2 están influenciadas por su interacción con otros estreses, como por ejemplo la salinidad, debido al creciente aumento de las áreas afectadas por la salinidad y su impacto sobre la masa vegetal. Por ello, en esta Tesis, se expone como la agricultura desarrolla una función muy importante en la lucha contra el cambio climático debido a su papel como secuestradores de CO2 atmosférico. Las conclusiones de este trabajo ayudarán a clarificar aspectos esenciales para elegir las soluciones más efectivas en este ámbito junto con otras problemáticas dadas en nuestras tierras de cultivos como son el estrés salino, el cual se verá implementado por dicho cambio climático. / CO2 is a variable key that affects both development and the plant physiology, so that the increases resulting from climate change will affect crop growth. Many of the observed physiological responses to increased CO2 in front are influenced by its interaction with other stresses, such as salinity, due to the increasing of the areas affected by the salinity and its impact on the vegetation. Therefore, in this thesis agriculture is exposed as a very important place in the fight against climate change due to its role as kidnappers of atmospheric CO2. The conclusions of this work help clarify what is essential to choose the best solutions effective in this area along with other issues given in our crop lands such as salt stress, which will be implemented by the climate change

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